knitr::opts_chunk$set(
echo = F,
message = F,
warning = F,
collapse = T
)
library(here)
## here() starts at /Users/nmedina/Documents/u/0/art/res/GitHub/osa
#.GlobalEnv::
source(
here("analysis/statsTbl.R")
)
## Registered S3 methods overwritten by 'readr':
## method from
## as.data.frame.spec_tbl_df vroom
## as_tibble.spec_tbl_df vroom
## format.col_spec vroom
## print.col_spec vroom
## print.collector vroom
## print.date_names vroom
## print.locale vroom
## str.col_spec vroom
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## ✓ tibble 3.1.4 ✓ dplyr 1.0.7
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## Using user data cache /Users/nmedina/Library/Application Support/R/BIOMASS
## To clear or remove cache see function clearCache().
## Rows: 1243 Columns: 17
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (3): fam, gen, sp
## dbl (14): ID, dist, plot, rep, N, W, incl, side, spg, dap, h, b, kg, luz
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Cache last modification time : 2021-01-06 15:19:51
## Source cache:1242
## Corrections FALSE:936, TaxaNotFound:212, TRUE:7, SpNotFound:87
## The reference dataset contains 16467 wood density values
## Your taxonomic table contains 49 taxa
##
## Attaching package: 'rstatix'
## The following object is masked from 'package:stats':
##
## filter
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.5-7
## Adding missing grouping variables: `dist`, `plot`
## Adding missing grouping variables: `dist`, `plot`, `fam`, `gen`, `sp`
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## print.nullmodel vegan
## Registered S3 method overwritten by 'tune':
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## • Use tidymodels_prefer() to resolve common conflicts.
## Loading required package: ggpp
##
## Attaching package: 'ggpp'
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## annotate
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spg et al. vars at tree or plot level? i think plot level.
richness, entropy [+spg] signif
but why reverse relationships from each other?
check curve below
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## Call:
## adonis(formula = ordModel, data = metaTbl, permutations = 99999)
##
## Permutation: free
## Number of permutations: 99999
##
## Terms added sequentially (first to last)
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## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## dist 1 0.6074 0.60742 3.6008 0.11395 0.00214 **
## Residuals 28 4.7234 0.16869 0.88605
## Total 29 5.3308 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
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